Hello gmxusers !! I am simulating a protein and it is bound to ATP. Simulation of protein alone (without) works fine. Solely ATP simulation too works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) file. Error:
$ genion -s em.tpr -o ion.pdb -p topol.top -np 48 WARNING: turning of free energy, will use lambda=0 Reading file em.tpr, VERSION 4.0.7 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 48 Na ions and 0 Cl ions. Select a continuous group of solvent molecules Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 70056 elements Group 1 ( Protein) has 10214 elements Group 2 ( Protein-H) has 5107 elements Group 3 ( C-alpha) has 623 elements Group 4 ( Backbone) has 1869 elements Group 5 ( MainChain) has 2488 elements Group 6 (MainChain+Cb) has 3083 elements Group 7 ( MainChain+H) has 3099 elements Group 8 ( SideChain) has 7115 elements Group 9 ( SideChain-H) has 2619 elements Group 10 ( Prot-Masses) has 10214 elements Group 11 ( Non-Protein) has 59842 elements Group 12 ( ATP) has 43 elements Group 13 ( SOL) has 59799 elements Group 14 ( Other) has 59842 elements Select a group: 13 Selected 13: 'SOL' Number of (3-atomic) solvent molecules: 19933 Processing topology Back Off! I just backed up temp.top to ./#temp.top.1# ------------------------------------------------------- Program genion, VERSION 4.0.7 Source code file: gmx_genion.c, line: 269 Software inconsistency error: Not enough water ------------------------------------------------------- Though my system has sufficient amount of water (19933) molecules. Can not understand the error. Any information would be useful. Chadan -- Chandan kumar Choudhury NCL, Pune INDIA
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